ArticleGigaScience2018
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed.
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- Large DNA and protein language models enhance discovery of deleterious mutations in maize.Genome biology · 2025Article
- Bayesian reconstruction and differential testing of excised introns.Bioinformatics (Oxford, England) · 2025Article
- Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population.Molecular biology and evolution · 2025Article
- A chromosome-level assembly and functional genomic resources for the model annelidbioRxiv : the preprint server for biology · 2025Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- Widespread 3' UTR splicing regulates expression of oncogene transcripts through multiple mechanisms.Nucleic acids research · 2025Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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Abstract
Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed; however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Here, we describe the extent of this problem using popular RNA-seq mapping tools and present a new method, called Portcullis, to rapidly filter false SJs derived from spliced alignments. We show that Portcullis distinguishes between genuine and false-positive junctions to a high degree of accuracy across different species, samples, expression levels, error profiles, and read lengths. Portcullis is portable, efficient, and, to our knowledge, currently the only SJ prediction tool that reliably scales for use with large RNA-seq datasets and large, highly fragmented genomes, while delivering accurate SJs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.